The large scale study of biological systems via the analysis of the protein complement, or ‘proteomics’, is increasingly dependent on the ability to rapidly screen complex mixtures of proteins in sensitive and efficient manners. As a result, the understanding of protein function in biological systems using large-scale proteomic approaches often pushes the limits of current analytical capabilities1-5, in particular, that of protein separation and protein analysis by mass spectrometry. Arguably, the identification and quantification of a diverse array of protein expression represents the most significant challenge. Often conventional approaches such as two-dimensional poly acrylamide gels (2D-PAGE), even when coupled to mass spectrometry are limited in their utility for the identification and quantification of protein expression in samples.6 Alternative approaches based on multidimensional chromatography coupled to mass spectrometry (‘gel free approaches’) have shown promising results; however, the lack of quantitation tools will also hamper the future of these approaches.7-10 
Regardless of the platform employed, the identification of proteins usually relies on mass spectrometry based analysis. Over the years, matrix assisted laser desorption/ionization (MALDI)11 and electrospray ionization12 based mass spectrometers have come to dominate the field. In particular, the recently introduced orthogonal MALDI quadrupole time of flight mass spectrometer (QqTOF),13-16 ESI ion trap mass spectrometers17 and ESI quadrupole—quadrupole time of flight (QqTOF) mass spectrometers18 have changed the approach to proteomics. As such, the challenges now lie in the preprocessing of samples (such as sample multiplexing and quantitative labeling) and post processing of the information (e.g. search algorithms and data-basing) rather than the nature of the ion-source.
The abilities to multiplex and to perform relative quantitation of protein samples are clearly not addressed by current proteomic technology. The needs are threefold: I) technology that allows for the differential labeling of protein samples so that their origin can be differentiated from other samples that have been mixed or pooled in the same sample, II) technology that can be used for rapid proteomic process prototyping, and II) technology that provides relative quantitation of protein levels based on mass spectrometric read-out. For example, the differential isotopic labeling of samples produces distinct isotopic patterns that can be identified through mass spectrometric measurements. This would allow multiple samples to be run at one time while still maintaining sample tracking information. In addition, process development in proteomics has typically been constrained to the use of radioactive elements for quantitative assessment. Numerous parameters have been described in the literature to influence the success of MS based proteomic approaches. Therefore, the development of novel technology that can be routinely used to assess the efficiency of sample handling and processing steps is critical for the improvement of high throughput proteomic analysis processes. Furthermore, the development of relative quantitation technology based on the analysis of peptides by mass spectrometry is primordial to the rapid analysis of the analysis of the differential expression of proteins in different tissue samples (disease vs. normal), between different cell lines or differently stimulated cell lines.